- API Allow passing arguments to [first_level_from_bids](https://nilearn.github.io/dev/modules/generated/nilearn.glm.first_level.first_level_from_bids.html#nilearn.glm.first_level.first_level_from_bids) to build first level models that include specific set of confounds by relying on the strategies from [load_confounds](https://nilearn.github.io/dev/modules/generated/nilearn.interfaces.fmriprep.load_confounds.html#nilearn.interfaces.fmriprep.load_confounds) ([4103](https://github.com/nilearn/nilearn/issues/4103) by [Rémi Gau](https://github.com/Remi-Gau)).
- Support passing t and F contrasts to [compute_contrast](https://nilearn.github.io/dev/modules/generated/nilearn.glm.compute_contrast.html#nilearn.glm.compute_contrast) that that have fewer columns than the number of estimated parameters. Remaining columns are padded with zero ([4067](https://github.com/nilearn/nilearn/issues/4067) by [Rémi Gau](https://github.com/Remi-Gau)).
- [NiftiSpheresMasker](https://nilearn.github.io/dev/modules/generated/nilearn.maskers.NiftiSpheresMasker.html#nilearn.maskers.NiftiSpheresMasker) now has generate_report method ([3102](https://github.com/nilearn/nilearn/issues/3102) by [Yasmin Mzayek](https://github.com/ymzayek) and [Nicolas Gensollen](https://nicolasgensollen.github.io/)).
- Update the CompCor strategy in [load_confounds](https://nilearn.github.io/dev/modules/generated/nilearn.interfaces.fmriprep.load_confounds.html#nilearn.interfaces.fmriprep.load_confounds) and [load_confounds_strategy](https://nilearn.github.io/dev/modules/generated/nilearn.interfaces.fmriprep.load_confounds_strategy.html#nilearn.interfaces.fmriprep.load_confounds_strategy) to support fmriprep 21.x series and above. ([3285](https://github.com/nilearn/nilearn/issues/3285) by [Hao-Ting Wang](https://wanghaoting.com/)).
- Allow setting vmin in [plot_glass_brain](https://nilearn.github.io/dev/modules/generated/nilearn.plotting.plot_glass_brain.html#nilearn.plotting.plot_glass_brain) and [plot_stat_map](https://nilearn.github.io/dev/modules/generated/nilearn.plotting.plot_stat_map.html#nilearn.plotting.plot_stat_map) ([3993](https://github.com/nilearn/nilearn/issues/3993) by [Michelle Wang](https://github.com/michellewang)).
- When plotting thresholded statistical maps with a colorbar, the threshold value(s) will now be displayed as tick labels on the colorbar ([2833](https://github.com/nilearn/nilearn/#2833) by [Nicolas Gensollen](https://nicolasgensollen.github.io/)).
- Combine GLM examples plot_fixed_effect and plot_fiac_analysis into a a single example plot_two_runs_model ([3191](https://github.com/nilearn/nilearn/issues/3191) by [Taylor Salo](https://tsalo.github.io/) and [Rémi Gau](https://github.com/Remi-Gau)).
NEW
- The temp_file_lifetime parameter of interactive plots’ open_in_browser method is deprecated and has no effect ([4180](https://github.com/nilearn/nilearn/issues/4180) by [Jerome Dockes](https://jeromedockes.github.io/))..
Fixes
- [MultiNiftiMasker](https://nilearn.github.io/dev/modules/generated/nilearn.maskers.MultiNiftiMasker.html#nilearn.maskers.MultiNiftiMasker) can now call [generate_report](https://nilearn.github.io/dev/modules/generated/nilearn.maskers.NiftiMasker.html#nilearn.maskers.NiftiMasker.generate_report) which will generate a report for the first subject in the list of subjects ([4001](https://github.com/nilearn/nilearn/issues/4001) by [Yasmin Mzayek](https://github.com/ymzayek)).
- Make sure that all atlases and datasets fetchers return a description ([4215](https://github.com/nilearn/nilearn/issues/4215) [Rémi Gau](https://github.com/Remi-Gau)).
- Update the CompCor strategy in [load_confounds](https://nilearn.github.io/dev/modules/generated/nilearn.interfaces.fmriprep.load_confounds.html#nilearn.interfaces.fmriprep.load_confounds) and [load_confounds_strategy](https://nilearn.github.io/dev/modules/generated/nilearn.interfaces.fmriprep.load_confounds_strategy.html#nilearn.interfaces.fmriprep.load_confounds_strategy) to support fmriprep 21.x series and above. ([3285](https://github.com/nilearn/nilearn/issues/3285) by [Hao-Ting Wang](https://wanghaoting.com/)).
- Fix [SimpleRegressionResults](https://nilearn.github.io/dev/modules/generated/nilearn.glm.SimpleRegressionResults.html#nilearn.glm.SimpleRegressionResults) to accommodate for the lack of a model attribute ([4071](https://github.com/nilearn/nilearn/issues/4071) [Rémi Gau](https://github.com/Remi-Gau))
- [clean_img](https://nilearn.github.io/dev/modules/generated/nilearn.image.clean_img.html#nilearn.image.clean_img) can now use kwargs clean__sample_mask argument to correctly reshape the nifti image to the dimensions of the mask in the output ([4051](https://github.com/nilearn/nilearn/issues/4051) by [Mia Zwally](https://github.com/MIZwally)).
- Fix plotting of an image with color bar when maximum value is exactly zero ([4204](https://github.com/nilearn/nilearn/issues/4204) by [Rémi Gau](https://github.com/Remi-Gau)).
- Code Fix PSC normalisation method applied by standardize_signal in [signal](https://nilearn.github.io/dev/modules/signal.html#module-nilearn.signal) ([4116](https://github.com/nilearn/nilearn/issues/4116) by [Hao-Ting Wang](https://wanghaoting.com/) and [Yasmin Mzayek](https://github.com/ymzayek)).
- Fixed inheritance of decoder classes to keep compatibility with scikit-learn>v1.3 ([4188](https://github.com/nilearn/nilearn/issues/4188) by [Yasmin Mzayek](https://github.com/ymzayek)).
- Make sure that all the fetchers for atlas and func from [nilearn.datasets](https://nilearn.github.io/dev/modules/datasets.html#module-nilearn.datasets) return a [sklearn.utils.Bunch](https://scikit-learn.org/stable/modules/generated/sklearn.utils.Bunch.html#sklearn.utils.Bunch). Add new behavior to [fetch_language_localizer_demo_dataset](https://nilearn.github.io/dev/modules/generated/nilearn.datasets.fetch_language_localizer_demo_dataset.html#nilearn.datasets.fetch_language_localizer_demo_dataset) to return output as Bunch. This behavior will become the default in version 0.13.0 ([4233](https://github.com/nilearn/nilearn/issues/4233) by [Rémi Gau](https://github.com/Remi-Gau)).
Enhancements
- [NiftiSpheresMasker](https://nilearn.github.io/dev/modules/generated/nilearn.maskers.NiftiSpheresMasker.html#nilearn.maskers.NiftiSpheresMasker) now has generate_report method ([3102](https://github.com/nilearn/nilearn/issues/3102) by [Yasmin Mzayek](https://github.com/ymzayek) and [Nicolas Gensollen](https://nicolasgensollen.github.io/)).
- Allow passing Pandas Series of image filenames to [SecondLevelModel](https://nilearn.github.io/dev/modules/generated/nilearn.glm.second_level.SecondLevelModel.html#nilearn.glm.second_level.SecondLevelModel) ([4070](https://github.com/nilearn/nilearn/issues/4070) by [Rémi Gau](https://github.com/Remi-Gau)).
- Allow passing arguments to [first_level_from_bids](https://nilearn.github.io/dev/modules/generated/nilearn.glm.first_level.first_level_from_bids.html#nilearn.glm.first_level.first_level_from_bids) to build first level models that include specific set of confounds by relying on the strategies from [load_confounds](https://nilearn.github.io/dev/modules/generated/nilearn.interfaces.fmriprep.load_confounds.html#nilearn.interfaces.fmriprep.load_confounds) ([4103](https://github.com/nilearn/nilearn/issues/4103) by [Rémi Gau](https://github.com/Remi-Gau)).
- Support passing t and F contrasts to [compute_contrast](https://nilearn.github.io/dev/modules/generated/nilearn.glm.compute_contrast.html#nilearn.glm.compute_contrast) that that have fewer columns than the number of estimated parameters. Remaining columns are padded with zero ([4067](https://github.com/nilearn/nilearn/issues/4067) by [Rémi Gau](https://github.com/Remi-Gau)).
- Multi-subject maskers’ generate_report method no longer fails with 5D data but instead shows report of first subject. User can index input list to show report for different subjects ([3935](https://github.com/nilearn/nilearn/issues/3935) by [Yasmin Mzayek](https://github.com/ymzayek)).
- Allow global_signal parameter in [load_confounds_strategy](https://nilearn.github.io/dev/modules/generated/nilearn.interfaces.fmriprep.load_confounds_strategy.html#nilearn.interfaces.fmriprep.load_confounds_strategy) in denoise_strategy='compcor' ([4225](https://github.com/nilearn/nilearn/issues/4225) by [Hao-Ting Wang](https://wanghaoting.com/)).
- Add two_sided option for [binarize_img](https://nilearn.github.io/dev/modules/generated/nilearn.image.binarize_img.html#nilearn.image.binarize_img) ([4121](https://github.com/nilearn/nilearn/issues/4121) by [Steven Meisler](https://www.stevenmeisler.com/)).
- [generate_report](https://nilearn.github.io/dev/modules/generated/nilearn.maskers.NiftiLabelsMasker.html#nilearn.maskers.NiftiLabelsMasker.generate_report) now uses appropriate cut coordinates when functional image is provided ([4099](https://github.com/nilearn/nilearn/issues/4099) by [Yasmin Mzayek](https://github.com/ymzayek) and [Nicolas Gensollen](https://nicolasgensollen.github.io/)).
- Mention the classification type (all-vs-one) in [Decoding of a dataset after GLM fit for signal extraction](https://nilearn.github.io/dev/auto_examples/02_decoding/plot_haxby_glm_decoding.html#sphx-glr-auto-examples-02-decoding-plot-haxby-glm-decoding-py) ([4122](https://github.com/nilearn/nilearn/issues/4122) by [Tamer Gezici](https://github.com/TamerGezici)).
- Add backslash to homogenize [Parcellations](https://nilearn.github.io/dev/modules/generated/nilearn.regions.Parcellations.html#nilearn.regions.Parcellations) documentation ([4042](https://github.com/nilearn/nilearn/issues/4042) by [Nikhil Krish](https://github.com/NIkhilgKrish)).
- Specify full form of LSS in [Beta-Series Modeling for Task-Based Functional Connectivity and Decoding](https://nilearn.github.io/dev/auto_examples/07_advanced/plot_beta_series.html#sphx-glr-auto-examples-07-advanced-plot-beta-series-py) ([4141](https://github.com/nilearn/nilearn/issues/4141) by [Tamer Gezici](https://github.com/TamerGezici)).
- Don’t fetch tmaps in examples if tmaps aren’t used in the example. ([4136](https://github.com/nilearn/nilearn/issues/4136) by [Christina Roßmanith](https://github.com/crossmanith)).
- Describe the return value in [fetch_abide_pcp](https://nilearn.github.io/dev/modules/generated/nilearn.datasets.fetch_abide_pcp.html#nilearn.datasets.fetch_abide_pcp) documentation ([4159](https://github.com/nilearn/nilearn/issues/4159) by [Suramya Pokharel](https://github.com/SuramyaP)).
- Allow setting vmin in [plot_glass_brain](https://nilearn.github.io/dev/modules/generated/nilearn.plotting.plot_glass_brain.html#nilearn.plotting.plot_glass_brain) and [plot_stat_map](https://nilearn.github.io/dev/modules/generated/nilearn.plotting.plot_stat_map.html#nilearn.plotting.plot_stat_map) ([3993](https://github.com/nilearn/nilearn/issues/3993) by [Michelle Wang](https://github.com/michellewang)).
- When plotting thresholded statistical maps with a colorbar, the threshold value(s) will now be displayed as tick labels on the colorbar ([2833](https://github.com/nilearn/nilearn/#2833) by [Nicolas Gensollen](https://nicolasgensollen.github.io/)).
Changes
- Expose scipy CubicSpline extrapolate parameter in [clean](https://nilearn.github.io/dev/modules/generated/nilearn.signal.clean.html#nilearn.signal.clean) to control the interpolation of censored volumes in both ends of the BOLD signal data ([4028](https://github.com/nilearn/nilearn/issues/4028) by [Jordi Huguet](https://github.com/jhuguetn)).
- Make nilearn.reporting._get_clusters_table module public and move copy_img out of nilearn._utils.niimg ([4166](https://github.com/nilearn/nilearn/issues/4166) by [Rémi Gau](https://github.com/Remi-Gau)).
- Private utility context manager write_tmp_imgs is refactored into function write_imgs_to_path ([4094](https://github.com/nilearn/nilearn/issues/4094) by [Yasmin Mzayek](https://github.com/ymzayek)).
- Move user facing function concat_niimgs out of private module nilearn._utils.niimg_conversions ([4167](https://github.com/nilearn/nilearn/issues/4167) by [Rémi Gau](https://github.com/Remi-Gau)).
- Remove leading underscore from non private functions to align with PEP8 ([4086](https://github.com/nilearn/nilearn/issues/4086) by [Rémi Gau](https://github.com/Remi-Gau)).
- Make decoding/proximal_operator explicitly private to align with PEP8 ([4153](https://github.com/nilearn/nilearn/issues/4153) by [Rémi Gau](https://github.com/Remi-Gau)).
- Make private functions public when used outside of their module nilearn.interface to align with PEP8 ([4168](https://github.com/nilearn/nilearn/issues/4168) by [Rémi Gau](https://github.com/Remi-Gau)).
- [img_to_signals_labels](https://nilearn.github.io/dev/modules/generated/nilearn.regions.img_to_signals_labels.html#nilearn.regions.img_to_signals_labels) will also return masked_atlas in release 0.15. Meanwhile, use return_masked_atlas parameter to enable/disable this behavior. ([3761](https://github.com/nilearn/nilearn/issues/3761) by [Mohammad Torabi](https://github.com/mtorabi59)).
- cation Rename the parameter contrast_type in [compute_contrast](https://nilearn.github.io/dev/modules/generated/nilearn.glm.compute_contrast.html#nilearn.glm.compute_contrast) and attribute contrast_type in [Contrast](https://nilearn.github.io/dev/modules/generated/nilearn.glm.Contrast.html#nilearn.glm.Contrast) to stat_type ([4191](https://github.com/nilearn/nilearn/issues/4191) by [Rémi Gau](https://github.com/Remi-Gau)).
- [plot_surf_roi](https://nilearn.github.io/dev/modules/generated/nilearn.plotting.plot_surf_roi.html#nilearn.plotting.plot_surf_roi) will raise a warning if roi_map contains negative or non-integer values; in version 0.13 this will be a ValueError ([4131](https://github.com/nilearn/nilearn/issues/4131) by [Michelle Wang](https://github.com/michellewang)).
- nilearn.datasets.fetch_bids_langloc_dataset will be deprecated in release 0.13 as it returns data simuilar to [fetch_language_localizer_demo_dataset](https://nilearn.github.io/dev/modules/generated/nilearn.datasets.fetch_language_localizer_demo_dataset.html#nilearn.datasets.fetch_language_localizer_demo_dataset) ([4219](https://github.com/nilearn/nilearn/issues/4219) by [Rémi Gau](https://github.com/Remi-Gau)).
- the default parameter of fd_threshold and std_dvars_threshold in [load_confounds](https://nilearn.github.io/dev/modules/generated/nilearn.interfaces.fmriprep.load_confounds.html#nilearn.interfaces.fmriprep.load_confounds) with be updated to match fmriprep default in version 0.13 ([4225](https://github.com/nilearn/nilearn/issues/4225) by [Hao-Ting Wang](https://wanghaoting.com/)).
- Combine GLM examples plot_fixed_effect and plot_fiac_analysis into a a single example plot_two_runs_model ([3191](https://github.com/nilearn/nilearn/issues/3191) by [Taylor Salo](https://tsalo.github.io/) and [Rémi Gau](https://github.com/Remi-Gau)).
- Switch to using tox to manage environments during development and testing. All plotting python dependencies (matplotlib AND plotly) are now installed when running pip install nilearn[plotting] ([4029](https://github.com/nilearn/nilearn/issues/4029) by [Rémi Gau](https://github.com/Remi-Gau)).
List of pull requests
* [MAINT] Post release 0.10.2 by Remi-Gau in https://github.com/nilearn/nilearn/pull/4022
* [FIX] fix spelling by Remi-Gau in https://github.com/nilearn/nilearn/pull/4026
* [MAINT] Add python 3.12 to CI by Remi-Gau in https://github.com/nilearn/nilearn/pull/4023
* [FIX] Allow `MultiNiftiMasker` to use `generate_report` method by ymzayek in https://github.com/nilearn/nilearn/pull/4001
* [MAINT] Implement deprecation warnings-as-errors in prerelease test using pytest fixture by ymzayek in https://github.com/nilearn/nilearn/pull/3936
* [MAINT] Ignore private visual testing file when running pytest by ymzayek in https://github.com/nilearn/nilearn/pull/4030
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4041
* [DOC] Change all block splitters in examples to use short syntax by ymzayek in https://github.com/nilearn/nilearn/pull/4031
* [MAINT] Update issue labels by Remi-Gau in https://github.com/nilearn/nilearn/pull/4036
* [MAINT] Add partial build specific to CI doc build workflow by ymzayek in https://github.com/nilearn/nilearn/pull/4044
* [ENH] Allow setting `vmin` in `plot_glass_brain` and `plot_stat_map` by michellewang in https://github.com/nilearn/nilearn/pull/3993
* [MAINT] Use correct target name for Makefile recipe by ymzayek in https://github.com/nilearn/nilearn/pull/4045
* [MAINT] Rename and move testing utilities under tests directory in each module by ymzayek in https://github.com/nilearn/nilearn/pull/4047
* [MAINT] refactor is plotly installed by Remi-Gau in https://github.com/nilearn/nilearn/pull/4034
* [FIX] fix typos in Harvard Oxford atlas labels by Remi-Gau in https://github.com/nilearn/nilearn/pull/4035
* [ENH] add readme to default data locations by Remi-Gau in https://github.com/nilearn/nilearn/pull/4037
* [DOC] link terms to glossary by Remi-Gau in https://github.com/nilearn/nilearn/pull/4038
* [DOC] update URLs with `http://` to `https://` by DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4050
* [DOC] Fix wrong indentation of example code by ymzayek in https://github.com/nilearn/nilearn/pull/4053
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4058
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4059
* [MAINT] Use rng fixture for setting up np.random.RandomState() - part 2 by ymzayek in https://github.com/nilearn/nilearn/pull/4054
* [MAINT] use affine_eye fixture by Remi-Gau in https://github.com/nilearn/nilearn/pull/4056
* [MAINT] Refactor fixture for plotting by Remi-Gau in https://github.com/nilearn/nilearn/pull/4057
* [DOC] move default from end of argument description to type name by Remi-Gau in https://github.com/nilearn/nilearn/pull/4040
* [MAINT fix typo in fixture name by Remi-Gau in https://github.com/nilearn/nilearn/pull/4062
* [MAINT] Pytest fixture to ignore internal deprecation warnings by ymzayek in https://github.com/nilearn/nilearn/pull/4043
* [MAINT] change function privacy in _utils by Remi-Gau in https://github.com/nilearn/nilearn/pull/4061
* [MAINT] change future warning to deprecation warning by Remi-Gau in https://github.com/nilearn/nilearn/pull/4060
* [MAINT] Use rng fixture for setting up `np.random.RandomState()` - part 1 by ymzayek in https://github.com/nilearn/nilearn/pull/4052
* [FIX] fix experimental example private function in monkeypatch by Remi-Gau in https://github.com/nilearn/nilearn/pull/4065
* [DOC] Formatting of docstring in regions.Parcellations by NIkhilgKrish in https://github.com/nilearn/nilearn/pull/4042
* [MAINT] Use rng fixture instead of check_random_state by Remi-Gau in https://github.com/nilearn/nilearn/pull/4063
* [STY] Minor doc formatting by Remi-Gau in https://github.com/nilearn/nilearn/pull/4072
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4075
* [ENH] Allow pandas.Series as valid input for second_level_input by Remi-Gau in https://github.com/nilearn/nilearn/pull/4070
* [ENH] pad t and F 'short' contrasts with zeros by Remi-Gau in https://github.com/nilearn/nilearn/pull/4067
* [DOC] Fix failing docs on main by ymzayek in https://github.com/nilearn/nilearn/pull/4079
* [MAINT] refactor of tests and code in GLM module by Remi-Gau in https://github.com/nilearn/nilearn/pull/4066
* [MAINT] drop python 3.7 by Remi-Gau in https://github.com/nilearn/nilearn/pull/4033
* [DOC] Make scope limit more obvious regarding accepting new downloaders by Remi-Gau in https://github.com/nilearn/nilearn/pull/4080
* [DOC][MAINT] Remove restriction on Sphinx version by ymzayek in https://github.com/nilearn/nilearn/pull/4081
* [FIX] image.clean_img() kwargs integration by MIZwally in https://github.com/nilearn/nilearn/pull/4051
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4083
* [FIX] fix typo by Remi-Gau in https://github.com/nilearn/nilearn/pull/4091
* [MAINT] update DOI and add RRID by Remi-Gau in https://github.com/nilearn/nilearn/pull/4032
* [DOC] mention checking badges during release by Remi-Gau in https://github.com/nilearn/nilearn/pull/4085
* [MAINT] Fix Zenodo DOI badge by ymzayek in https://github.com/nilearn/nilearn/pull/4093
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4097
* [DOC] Remove extraneous hash symbols for examples' section splitters by ymzayek in https://github.com/nilearn/nilearn/pull/4096
* [DOC] Improve docstring rendering for typed experimental surface module by ymzayek in https://github.com/nilearn/nilearn/pull/4049
* [DOC] Add tagging of release version to stable doc build by ymzayek in https://github.com/nilearn/nilearn/pull/4100
* [FIX] Disable extrapolation of out-of-bounds volumes by jhuguetn in https://github.com/nilearn/nilearn/pull/4028
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4102
* [MAINT] Add listing utilities by NicolasGensollen in https://github.com/nilearn/nilearn/pull/2991
* [MAINT] Pin kaleido version to `0.1.0.post1` for windows by ymzayek in https://github.com/nilearn/nilearn/pull/4101
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4105
* [MAINT] Rewrite `write_tmp_imgs` function and use it with pytest's `tmp_path` by ymzayek in https://github.com/nilearn/nilearn/pull/4094
* [MAINT] Use Numpy Random Generator to replace legacy RandomState by ymzayek in https://github.com/nilearn/nilearn/pull/4084
* [MAINT] Store 1 timepoint for 4D generating a report with the maskers by ymzayek in https://github.com/nilearn/nilearn/pull/3935
* [DOC] Speed up fit computation with parallel processing by ymzayek in https://github.com/nilearn/nilearn/pull/4108
* [REF] Clarify code in `find_parcellation_cut_coords` function by ymzayek in https://github.com/nilearn/nilearn/pull/4107
* [MAINT] using tox to test in different environments by Remi-Gau in https://github.com/nilearn/nilearn/pull/4029
* [DOC] Fix label in changelog by Remi-Gau in https://github.com/nilearn/nilearn/pull/4114
* [DOC] Clarify docstrings of plotting functions in `img_plotting` by ymzayek in https://github.com/nilearn/nilearn/pull/4115
* [EHN] Implement signal.clean to SurfaceMasker by htwangtw in https://github.com/nilearn/nilearn/pull/4117
* [ENH] Update binarize_img for negative value handling by smeisler in https://github.com/nilearn/nilearn/pull/4121
* [ENH] Colorbar ticks at threshold values by NicolasGensollen in https://github.com/nilearn/nilearn/pull/2887
* [ENH] Add new returns to `NiftiLabelsMasker`'s `transform` output by mtorabi59 in https://github.com/nilearn/nilearn/pull/3761
* [ENH] Set appropriate cut coordinates for NiftiLabelsMasker reports by ymzayek in https://github.com/nilearn/nilearn/pull/4099
* [MAINT] minor pre-commit fix by Remi-Gau in https://github.com/nilearn/nilearn/pull/4125
* [ENH] Let _check_embedded_nifti_masker work with surface masker by ymzayek in https://github.com/nilearn/nilearn/pull/4120
* [MAINT] Test against Numpy 2.0 nightly releases by ymzayek in https://github.com/nilearn/nilearn/pull/4130
* [MAINT] Remove trigger on PR for numpy2 test by ymzayek in https://github.com/nilearn/nilearn/pull/4133
* [DOC] Mention classification type in plot_haxby_glm_decoding.py by TamerGezici in https://github.com/nilearn/nilearn/pull/4122
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4134
* [MAINT] remove leading underscore from non private functions by Remi-Gau in https://github.com/nilearn/nilearn/pull/4086
* [ENH] `NiftiSpheresMasker` reports by NicolasGensollen in https://github.com/nilearn/nilearn/pull/3102
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4142
* Bump actions/setup-python from 4 to 5 by dependabot in https://github.com/nilearn/nilearn/pull/4143
* Don't use get_tmaps=True if tmaps aren't used by crossmanith in https://github.com/nilearn/nilearn/pull/4136
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4148
* [ENH] Raise error when negative or non-integer ROI values are passed to `plot_surf_roi` by michellewang in https://github.com/nilearn/nilearn/pull/4131
* [DOC] Specify full form of LSS in beta series tutorial by TamerGezici in https://github.com/nilearn/nilearn/pull/4141
* [MAINT] Apply Black to nifti_labels_masker.py by ymzayek in https://github.com/nilearn/nilearn/pull/4146
* [MAINT] Apply Black to reporting files by ymzayek in https://github.com/nilearn/nilearn/pull/4145
* [MAINT] Apply Black img_plotting.py by ymzayek in https://github.com/nilearn/nilearn/pull/4147
* [INFRA] Remove CI workflow to error on DeprecationWarnings of dependencies by ymzayek in https://github.com/nilearn/nilearn/pull/4149
* [MAINT] Apply Black to nifti_spheres_masker.py by ymzayek in https://github.com/nilearn/nilearn/pull/4144
* [MAINT] Improve error for nifti masker when fit is called without imgs or mask_img by ymzayek in https://github.com/nilearn/nilearn/pull/4151
* [MAINT] make proximal_operator a private module by Remi-Gau in https://github.com/nilearn/nilearn/pull/4153
* [ENH] rename `nilearn.datasets._utils.fetch_file` to `nilearn.datasets._utils.fetch_single_file` by Remi-Gau in https://github.com/nilearn/nilearn/pull/4156
* [MAINT] make `__all__` and API doc more consistent by Remi-Gau in https://github.com/nilearn/nilearn/pull/4157
* [MAINT] relocate functions from nilearn.datasets.utils by Remi-Gau in https://github.com/nilearn/nilearn/pull/4154
* [FIX] Load compcor related confounds generated from fmriprep 21.x series by htwangtw in https://github.com/nilearn/nilearn/pull/3285
* [STY] run black on nilearn/interfaces/fmriprep by Remi-Gau in https://github.com/nilearn/nilearn/pull/4163
* [FIX] Adjust figure size to display title for functions calling `plot_surf` by ymzayek in https://github.com/nilearn/nilearn/pull/4164
* [FIX] fix SimpleRegressionResults by Remi-Gau in https://github.com/nilearn/nilearn/pull/4071
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4169
* [ENH] integrate load_confounds into first_level_from_bids by Remi-Gau in https://github.com/nilearn/nilearn/pull/4103
* Bump actions/upload-artifact from 3 to 4 by dependabot in https://github.com/nilearn/nilearn/pull/4170
* Updated docs for fetch_abide_pcp by SuramyaP in https://github.com/nilearn/nilearn/pull/4159
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4174
* [MAINT] nilearn.interface: make private functions used outside of their module public by Remi-Gau in https://github.com/nilearn/nilearn/pull/4168
* [DOC] link surface terms to glossary by Remi-Gau in https://github.com/nilearn/nilearn/pull/4161
* [STY] apply black to `nilearn._utils.data_gen` by Remi-Gau in https://github.com/nilearn/nilearn/pull/4171
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4179
* [INFRA] Proposal for building stable docs in remote runner for releases by ymzayek in https://github.com/nilearn/nilearn/pull/4160
* [INFRA] Quick fix for automated stable doc build by ymzayek in https://github.com/nilearn/nilearn/pull/4181
* [INFRA] Fix auto trigger for release doc build in Actions workflow by ymzayek in https://github.com/nilearn/nilearn/pull/4182
* [FIX] use a local server rather than temp file to open plots in a browser by jeromedockes in https://github.com/nilearn/nilearn/pull/4180
* [FIX] rich display in jupyter notebook/lab by jeromedockes in https://github.com/nilearn/nilearn/pull/4183
* [MAINT] move user facing functions out of private modules by Remi-Gau in https://github.com/nilearn/nilearn/pull/4166
* [MAINT] move user facing functions out of private modules - part 2 by Remi-Gau in https://github.com/nilearn/nilearn/pull/4167
* [FIX] use parameter deprecation decorator by Remi-Gau in https://github.com/nilearn/nilearn/pull/4189
* [BOT] update pre-commit hooks by github-actions in https://github.com/nilearn/nilearn/pull/4193
* [STY] deal with private functions in nilearn.glm that do not coform to PEP8 naming by Remi-Gau in https://github.com/nilearn/nilearn/pull/4190
* [ENH] Allow string expressions for `second_level_contrast` of `non_parametric_inference` by ymzayek in https://github.com/nilearn/nilearn/pull/4150
* [FIX] rename `contrast_type` to `stat_type` by Remi-Gau in https://github.com/nilearn/nilearn/pull/4191
* [DOC] fix edit button for examples by Remi-Gau in https://github.com/nilearn/nilearn/pull/4196
* [MAINT] remove duplicate dependency by Remi-Gau in https://github.com/nilearn/nilearn/pull/4199
* [MAINT] remove some old mention of nistats by Remi-Gau in https://github.com/nilearn/nilearn/pull/4200
* [MAINT] make private functions in `nilearn.plotting` used outside of their module public by Remi-Gau in https://github.com/nilearn/nilearn/pull/4197
* [MAINT] testing minimal version of dependencies by Remi-Gau in https://github.com/nilearn/nilearn/pull/4068
* [MAINT] sort changelog by labels by Remi-Gau in https://github.com/nilearn/nilearn/pull/4201
* [MAINT] Remove unnecessary lines describe in `test_clean_psc` by paul-reiners in https://github.com/nilearn/nilearn/pull/4208
* [BOT] update AUTHORS.rst and doc/changes/names.rst by github-actions in https://github.com/nilearn/nilearn/pull/4213
* [DOC] format citation by Remi-Gau in https://github.com/nilearn/nilearn/pull/4212
* [DOC] replace `session` by `run` to align with BIDS terminology by Remi-Gau in https://github.com/nilearn/nilearn/pull/4214
* Bump actions/setup-python from 4 to 5 by dependabot in https://github.com/nilearn/nilearn/pull/4217
* [FIX] fix plotting of an image with color bar when maximum value is exactly zero by Remi-Gau in https://github.com/nilearn/nilearn/pull/4204
* [FIX] Fix PSC normalization when a high-pass filter is applied by ymzayek in https://github.com/nilearn/nilearn/pull/4116
* [MAINT] Adapt decoder for scikit-learn > 1.3 by ymzayek in https://github.com/nilearn/nilearn/pull/4188
* [DOC] update dataset descriptions by Remi-Gau in https://github.com/nilearn/nilearn/pull/4215
* [DOC] Combine similar two-runs GLM examples by tsalo in https://github.com/nilearn/nilearn/pull/3191
* [MAINT] speed up tests for html reports by Remi-Gau in https://github.com/nilearn/nilearn/pull/4221
* [DEP] deprecate bids_langloc fetcher by Remi-Gau in https://github.com/nilearn/nilearn/pull/4219
* FIX/EHN update load_confound_strategy defaults by htwangtw in https://github.com/nilearn/nilearn/pull/4225
* [FIX] Let decoder accept list of paths as input by ymzayek in https://github.com/nilearn/nilearn/pull/4227
* [FIX] Ensure that fetchers for atlas and func return a Bunch by Remi-Gau in https://github.com/nilearn/nilearn/pull/4233
* [MAINT] Examples output all their results in a single main directory by Remi-Gau in https://github.com/nilearn/nilearn/pull/4230
* Bump actions/cache from 3 to 4 by dependabot in https://github.com/nilearn/nilearn/pull/4234
* [DOC] update version in sphinx directives by Remi-Gau in https://github.com/nilearn/nilearn/pull/4238
* [DOC] sort changelog and add highlights by Remi-Gau in https://github.com/nilearn/nilearn/pull/4237
* [STY] apply black 24.1.0 by Remi-Gau in https://github.com/nilearn/nilearn/pull/4162
* [DOC] remove warning from experimental module and add it as doc string by Remi-Gau in https://github.com/nilearn/nilearn/pull/4240
* [STY] re apply black by Remi-Gau in https://github.com/nilearn/nilearn/pull/4241